Kinetic analysis of the interaction of alkyl glycosides with two human β-glucosidases

This paper addresses the similarities and differences in the topology of the catalytic centres of human liver cytosolic beta-glucosidase and placental lysosomal glucocerebrosidase, and utilizes well-documented reversible active-site-directed inhibitors. This comparative kinetic study was performed mainly to decipher the chemical and structural nature of the active site of the cytosolic beta-glucosidase, whose physiological function is unknown. Specifically, analysis of the effects of a family of alkyl beta-glucosides consistently displayed 100-250-fold lower inhibition constants with the cytosolic broad-specificity beta-glucosidase compared with the placental glucocerebrosidase; for example, with octyl beta-D-glucoside the Ki values were 10 microM and 1490 microM for the cytosolic and lysosomal beta-glucosidases respectively. Furthermore the higher affinity of the cytosolic beta-glucosidase than glucocerebrosidase for the amphipathic alkyl beta-D-glucosides was validated by the greater increase in the free energy of binding with increasing alkyl chain length [delta delta G0 (K,)/CH2: lysosomal enzyme, 2.01 kJ/mol (480 cal/mol); cytosolic enzyme, 3.05 kJ/mol (730 cal/mol)]. The implications of the presence of highly non-polar domains in the active site of the cytosolic beta-glucosidase are discussed with regard to its potential physiological substrates.

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Efficient laccase/TEMPO oxidation of alkyl glycosides: Effects of carbohydrate group and alkyl chain length

Journal of Biotechnology X ◽

10.1016/j.btecx.2020.100026 ◽

2020 ◽

Vol 8 ◽

pp. 100026

Author(s):

Ngoc T.N. Ngo ◽

Carl Grey ◽

Patrick Adlercreutz

Keyword(s):

Chain Length ◽

Alkyl Chain ◽

Alkyl Chain Length ◽

Tempo Oxidation ◽

Alkyl Glycosides

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Further studies on the substrate specificity and inhibition of the stereospecific CS2 secondary alkylsulphohydrolase of Comamonas terrigena

Biochemical Journal ◽

10.1042/bj1910467 ◽

1980 ◽

Vol 191 (2) ◽

pp. 467-473 ◽

Cited By ~ 13

Author(s):

Carol H. Barrett ◽

Kenneth S. Dodgson ◽

Graham F. White

Keyword(s):

Free Energy ◽

Chain Length ◽

Alkyl Chain ◽

Hydrophobic Interactions ◽

Standard Free Energy ◽

Alkyl Chain Length ◽

Alkyl Sulphate ◽

Competitive Inhibitors ◽

Free Energy Of Binding ◽

Comamonas Terrigena

A series of d-alkan-2-yl sulphate esters (C7–C14) were prepared by sulphation of the resolved parent alcohols by a method that entails complete retention of configuration. These sulphate esters were tested as substrates for the stereospecific CS2 secondary alkylsulphohydrolase of Comamonas terrigena. Vmax. reached a maximum with the C9 compound, whereas logKm decreased linearly as the alkyl-chain length was increased from C7 to C14. A parallel series of l-alkan-2-yl sulphates was also prepared, and these esters, together with homologous series of primary alkyl sulphates and primary alkanesulphonates, were shown to be competitive inhibitors of the CS2 enzyme. For each series of compounds, logKi values decreased linearly with increasing alkyl-chain length. Plots of chain length against the standard free energy of binding (ΔG0) of substrate and inhibitors to the CS2 enzyme showed that the standard free energy of association of a –CH2– group with the enzyme was 2.0–2.4kJ/mol for all classes of compound studied, indicating an important contribution from hydrophobic interactions to the overall binding. Plots for d-alkan-2-yl sulphate substrates and primary alkyl sulphate inhibitors were nearly coincident, suggesting that the overall interaction between a primary ester and the enzyme is the same as that between the isomeric secondary substrate and the enzyme. Plots for l-alkan-2-yl sulphate and alkanesulphonate inhibitors were very similar to each other, but were displaced by 1.5–3.0kJ/mol from that for substrate binding. This indicates that the binding of any one of these particular inhibitors involves one carbon atom fewer than the number involved in binding a substrate of the same chain length. These observations are discussed in terms of a three-point attachment of substrate to the enzyme involving the alkyl chain, sulphate group and the C-1 methyl group.

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In silico and in vitro studies of Imidazolium ionic liquids as effective antibacterial agents against multidrug resistant Escherichia coli strains

Current Bioactive Compounds ◽

10.2174/1573407216999200422115655 ◽

2020 ◽

Vol 16 ◽

Author(s):

Diana Hodyna ◽

Vasyl Kovalishyn ◽

Ivan Semenyuta ◽

Volodymyr Blagodatny ◽

Sergiy Rogalsky ◽

...

Keyword(s):

Escherichia Coli ◽

Antibacterial Activity ◽

Ionic Liquids ◽

Chain Length ◽

Active Site ◽

Alkyl Chain ◽

Multidrug Resistant ◽

Alkyl Chain Length ◽

E Coli

Background: Escherichia coli especially its multiresistant strains as the common foodborne pathogens cause blood stream infections, nosocomial pneumonia, infections of the skin and soft tissues. Therefore, the search for new effective biologically active compounds has been rapidly increasing in recent few decades. In this paper, we describe Quantitative Structure-Activity Relationships (QSAR) studies, molecular docking and in vitro antibacterial activity evaluation of series imidazolium-based ionic liquids (ILs) against E. coli spp. Methods: 2D fragment-based, classification and regression QSAR models were created using machine learning methods and types of descriptors via the OCHEM server. Biological testing of series of synthesized imidazolium ILs with predicted activity was performed by disc diffusion method. The most typical structures of symmetric and asymmetric ILs with high anti-E.coli activity (1e, 1h) were docked into the active site of enoylacyl carrier protein reductase (ENR) in E. coli. Results: Symmetric imidazolium ILs with C8 alkyl chain length demonstrated the highest antibacterial activity in comparison to the high antibacterial potential of asymmetric ILs with C12 alkyl chain length against drug-sensitive and drug-resistant E. coli strains including hemolytic E. coli. It should be noted that symmetric ILs with C6 or C9 alkyl chain length have the slightly lower activity against certain E. coli strains. The key role in the binding of compounds (1e, 1h) in the E. coli ENR active site associated with the NAD molecule and the amino acid residue Tyr146. Conclusion: The highly active symmetric and asymmetric imidazolium ILs can be considered as promising drug-candidates effective against E. coli spp. pathogens including multidrug resistant strains.

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Development of Xanthine Based Inhibitors Targeting Phosphodiesterase 9A

Letters in Drug Design & Discovery ◽

10.2174/1570180813666161102125423 ◽

2017 ◽

Vol 14 (10) ◽

pp. 1122-1137 ◽

Cited By ~ 1

Author(s):

Nivedita Singh ◽

Parameswaran Saravanan ◽

M.S. Thakur ◽

Sanjukta Patra

Keyword(s):

Free Energy ◽

Active Site ◽

Signal Transduction Pathway ◽

Docking Study ◽

Primary Objective ◽

Cgmp Level ◽

Active Site Residues ◽

Aromatic Fragment ◽

Docking Approach ◽

Free Energy Of Binding

Background: Phosphodiesterases 9A (PDE9A) is one of the prominent regulating enzymes of the signal transduction pathway having highest catalytic affinity for second messenger, cGMP. When the cGMP level is lowered, an uncontrolled expression of PDE9A may lead to various neurodegenerative diseases. To regulate the catalytic activity of PDE9A, potent inhibitors are needed. Objective: The primary objective of the present study was to develop new xanthine based inhibitors targeting PDE9A. This study was an attempt to bring structural diversification in PDE9A inhibitor development because most of the existing inhibitors are constructed over pyrazolopyrimidinone scaffold. Methods: Manual designing and parallel molecular docking approach were used for the development of xanthine derivatives. In this study, N1, N3, N9 and C8 positions of xanthine scaffold were selected as substitution sites to design 200 new compounds. Reverse docking and pharmaceutical analyses were used for final validation of most promising compounds. Results: By keeping free energy of binding cut-off of -6.0 kcal/mol, 52 compounds were screened. The compounds with substitution at N1, N3 and C8 positions of xanthine showed good occupancy in PDE9A active site pocket with a significant interaction pattern. This was further validated by screening different factors such as free energy of binding, inhibition constant and interacting active site residues in the 5Å region. Substitution at C8 position with phenyl substituent determined the inhibition affinity of compounds towards PDE9A by establishing a strong hydrophobic - hydrophobic interaction. The alkyl chain at N1 position generated selectivity of compounds towards PDE9A. The aromatic fragment at N3 position increased the binding affinity of compounds. Thus, by comparative docking study, it was found that compound 39-42 formed selective interaction towards PDE9A over other members of the PDE superfamily. Conclusion: From the present study, N1, N3 and C8 positions of xanthine were concluded as the best sites for substitution for the generation of potent PDE9A inhibitors.

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Influence of alkyl chain length on the action of acetylated monoglycerides as plasticizers for poly (vinyl chloride) food packaging film

Food Packaging and Shelf Life ◽

10.1016/j.fpsl.2020.100619 ◽

2021 ◽

Vol 27 ◽

pp. 100619

Author(s):

Chang Woo Kwon ◽

Pahn-Shick Chang

Keyword(s):

Chain Length ◽

Vinyl Chloride ◽

Food Packaging ◽

Alkyl Chain ◽

Alkyl Chain Length ◽

Packaging Film ◽

Poly Vinyl Chloride

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Silver Nanoparticles Stabilized with Phosphorus-Containing Heterocyclic Surfactants: Synthesis, Physico-Chemical Properties, and Biological Activity Determination

Nanomaterials ◽

10.3390/nano11081883 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1883

Author(s):

Martin Pisárčik ◽

Miloš Lukáč ◽

Josef Jampílek ◽

František Bilka ◽

Andrea Bilková ◽

...

Keyword(s):

Silver Nanoparticles ◽

Biological Activity ◽

Zeta Potential ◽

Chain Length ◽

Alkyl Chain ◽

Chemical Properties ◽

Alkyl Chain Length ◽

Microbial Pathogens ◽

Physico Chemical ◽

Phosphorus Containing

Phosphorus-containing heterocyclic cationic surfactants alkyldimethylphenylphospholium bromides with the alkyl chain length 14 to 18 carbon atoms were used for the stabilization of silver nanodispersions. Zeta potential of silver nanodispersions ranges from +35 to +70 mV, which indicates the formation of stable silver nanoparticles (AgNPs). Long-chain heptadecyl and octadecyl homologs of the surfactants series provided the most intensive stabilizing effect to AgNPs, resulting in high positive zeta potential values and smaller diameter of AgNPs in the range 50–60 nm. A comparison with non-heterocyclic alkyltrimethylphosphonium surfactants of the same alkyl chain length showed better stability and more positive zeta potential values for silver nanodispersions stabilized with heterocyclic phospholium surfactants. Investigations of biological activity of phospholium-capped AgNPs are represented by the studies of antimicrobial activity and cytotoxicity. While cytotoxicity results revealed an increased level of HepG2 cell growth inhibition as compared with the cytotoxicity level of silver-free surfactant solutions, no enhanced antimicrobial action of phospholium-capped AgNPs against microbial pathogens was observed. The comparison of cytotoxicity of AgNPs stabilized with various non-heterocyclic ammonium and phosphonium surfactants shows that AgNPs capped with heterocyclic alkyldimethylphenylphospholium and non-heterocyclic triphenyl-substituted phosphonium surfactants have the highest cytotoxicity among silver nanodispersions stabilized by the series of ammonium and phosphonium surfactants.

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